Now, here begins the realm of inter-fandom crossovers, in these situations, if I have a story appear in one fandom, that I later make a list for, that story won't appear in it. Because I'm lazy :-P

'Hazredous' Interruptions
By Eleventh Messenger
A Magical Girl Lyrical Nanoha/RWBY crossover
"Crippled in a battle with pirates beyond the edges of Administered Space, the TSAB Cruiser Arthra is forced to crash land on an unadministered world with a shattered moon. With no way to get a message out of the planet's strange field of interference, they're forced to seek help from someone in a position of power; Headmaster Ozpin of Beacon Academy."
Link: https://www.fanfiction.net/s/11755899/1/Hazredous-Interruptions

Shattered Skies
By: BHSDesk
"It's all gone wrong... An infinite darkness forces five universes to converge. Legendary magical girls from across time and space must unite to face a threat the likes of which none of them can imagine. A Sailor Moon / Cardcaptor Sakura / Precure All-Stars / Nanoha / Madoka Magica mega-crossover."
Link: https://www.fanfiction.net/s/10756548/1/Shattered-Skies
EDIT now on Wattpad!
http://my.w.tt/UiNb/puxxOkEW0F

Twist of Fate
By Skywalker-T65
"It is not an understatement to say that Nanoha, Fate and Homura have been through many dangerous experiences. However, none have been quite like this. For when Homura's attempt at resetting the timeline goes further and merges two worlds that should never have met...the situation can never be the same."
Link: https://www.fanfiction.net/s/11389765/1/Twist-of-Fate

Infinity
By Mozco
"The Book of Darkness case is over, giving Nanoha and company some much-needed rest. But the peace ends abruptly as a pair of unknown mages descend on Earth, seeking a lost artifact and reigniting an ancient conflict. It's time to save the world again..."
Link: https://www.fanfiction.net/s/5144486/1/Infinity

Nanoha Takamachi and the horrors of ineptitude"
By Silent-Scream84
"When the TSAB discovers the Wizarding World, Nanoha and Fate are sent to investigate. What will they learn about the HP universe and about themselves as they attend Hogwarts? Set during Order of The Phoenix."

Nanoha Takamachi and the School of Witchcraft"
By Ryvaken Lucius Tydra
"A few months after retiring home to England, former TSAB Admiral Graham finds himself attacked by men with pointy sticks and strange magic. He calls in help and sets Nanoha and Fate on a wild ride through the British Wizarding World. Book one of the Lyrical Witch series."
Link: https://www.fanfiction.net/s/8640163/1/Nanoha-Takamachi-and-the-School-of-Witchcraft

Nanoha Takamachi and the Wizarding World
By Ryvaken Lucius Tydra
"The White Devil is back at Hogwarts for another year, only this time she has to deal with a part time mage job as well as mysterious attacks, an old injustice, and a boy-hero who can't go two months without putting his life in danger. Book two of the Lyrical Witch series."
Link: https://www.fanfiction.net/s/10166402/1/Nanoha-Takamachi-and-the-Wizarding-World

ADDED as of 9/29/16, 10:54PM

Game Theory
By Immatrael
"Who dares stand between a mother and her daughter's life? Precia will do anything to achieve her goals. Even if it means accepting Fate. First of the Gamesverse series."
https://www.fanfiction.net/s/7485060/1/Game-Theory

Power Games
By Immatrael
"There's no such thing as happily ever after. Life goes on - even dearly bought. All Precia's plans may come to nought as shadowy actors take to the stage. But nothing unmasks a man like his use of power. Second of the Gamesverse series."
https://www.fanfiction.net/s/9156554/1/Power-Games

Fate T. Harlaown and the Case of the Murderous Murder
By Mozco
"When a regional governor falls prey to deadly murder, the TSAB sends in their elite investigator extraordinaire, Fate T. Harlaown, and her prime apprentice, Teana Lanster, to bring the killer to justice. But then they also send a third investigator, thus proving that while they've gotten a LITTLE better since the JS Incident, they still make mistakes."
https://www.fanfiction.net/s/9485532/1/Fate-T-Harlaown-and-the-Case-of-the-Murderous-Murder

Grand Tour
By DrunkenGrognard
"A crossover fic. Ryoga's curse of 'lost' threatens the fabric of the multiverse itself. The USS Voyager is swept up in his wake of chaos. The TSAB steps in to clean up the mess, recruiting Ranma to aid them, but it may already be too late to catch him..."
https://www.fanfiction.net/s/4869171/1/Grand-Tour

Journey
By DrunkenGrognard
"A sequel to Grand Tour. The Inner Senshi are off to Mid-Childa in pursuit of magical training, leaving the Outers to 'hold the fort' with a little help from a TSAB agent - Ranma Saotome. They aren't the only ones thinking of training..."
https://www.fanfiction.net/s/5418545/1/Journey

Odyssey
By DrunkenGrognard
"As an interdimensional war heats up, new factions emerge on the stage - what consequences will their actions have? Whose side are they on? And do they understand the forces involved? Part three of the Grand Tour series."
https://www.fanfiction.net/s/6081473/1/Odyssey

Walkabout
By DrunkenGrognard
"Part 4 of the Grand Tour series. Ranma decides that it's time to get his life in order. What could possibly go wrong?"
https://www.fanfiction.net/s/6576566/1/Walkabout